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(-) Description

Title :  SOLUTION STRUCTURE OF THE C-TERMINAL WRKY DOMAIN OF ATWRKY4
 
Authors :  K. Yamasaki, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dna-Binding Domain, Zinc-Binding, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, T. Yamasaki, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, Y. Tomo, N. Hayami, T. Terada, M. Shirouzu, A. Tanaka, M. Seki, K. Shinozaki, S. Yokoyama
Solution Structure Of An Arabidopsis Wrky Dna Binding Domain.
Plant Cell V. 17 944 2005
PubMed-ID: 15705956  |  Reference-DOI: 10.1105/TPC.104.026435
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE WRKY TRANSCRIPTION FACTOR 4
    ChainsA
    EngineeredYES
    Expression System PlasmidPCR2.1
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL WRKY DOMAIN
    GeneWRKY4
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Other DetailsCELL-FREE SYNTHESIS
    SynonymWRKY DNA-BINDING PROTEIN 4, WRKY4

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:434 , THR A:436 , CYS A:439 , HIS A:463 , HIS A:465BINDING SITE FOR RESIDUE ZN A 470

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WJ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WJ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WJ2)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WRKYPS50811 WRKY domain profile.WRKY4_ARATH229-287
403-468
  1-
A:403-468

(-) Exons   (0, 0)

(no "Exon" information available for 1WJ2)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:71
 aligned with WRKY4_ARATH | Q9XI90 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:71
                                   408       418       428       438       448       458       468 
          WRKY4_ARATH   399 VQTTSEVDLLDDGYRWRKYGQKVVKGNPYPRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNHDLPA 469
               SCOP domains d1wj2a_ A: WRKY DNA-binding protein 4                                   SCOP domains
               CATH domains 1wj2A00 A:399-469 Probable wrky transcription factor 4                  CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eee........eeeeeee....eeeeeeeee.....eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----WRKY  PDB: A:403-468 UniProt: 403-468                             - PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 1wj2 A 399 VQTTSEVDLLDDGYRWRKYGQKVVKGNPYPRSYYKCTTPGCGVRKHVERAATDPKAVVTTYEGKHNHDLPA 469
                                   408       418       428       438       448       458       468 

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WJ2)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (WRKY4_ARATH | Q9XI90)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:1900425    negative regulation of defense response to bacterium    Any process that stops, prevents or reduces the frequency, rate or extent of defense response to bacterium.
    GO:1900150    regulation of defense response to fungus    Any process that modulates the frequency, rate or extent of defense response to fungus.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009723    response to ethylene    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethylene (ethene) stimulus.
    GO:0009753    response to jasmonic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a jasmonic acid stimulus.
    GO:0009751    response to salicylic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salicylic acid stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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